Transport of karyophilic proteins into the nucleus is mediated by nuclear localization signals (NLSs) via a multistep process. The karyophiles are recognized by the importin alpha subunit in the cytoplasm to form a stable complex, termed the nuclear pore-targeting complex (PTAC). To date, three different mammalian alpha subunits (mSRP1/NPI-1, PTAC58/mPendulin/Rch1 and Qip1) have been identified. In this study, we report the identification of three additional mouse genes homologous to the known alpha subunits using RT-PCR methodology and show that the mouse alpha subunits can be classified into at least three subfamilies, alpha-P, alpha-Q and alpha-S families, each composed of closely related members (more than 80% amino acid sequence identity). These three subfamilies, however, have approximately 50% amino acid identity to one another. Northern blot analysis showed that all were differentially expressed in various mouse tissues. These results suggest that the function of these proteins may be controlled in a tissue-specific manner and that their combinatorial expression may play a role in differentiation and organogenesis.